Name: rs3214285
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs3214285

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:68540072-68540073 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: delAG
Variation Type: Deletion
Frequency: delAG=0.208701 (55241/264690, TOPMED)
delAG=0.215052 (30100/139966, GnomAD)
delAG=0.29882 (8444/28258, 14KJPN) (+ 11 more)
delAG=0.22559 (4178/18520, ALFA)
delAG=0.29433 (4933/16760, 8.3KJPN)
delAG=0.2097 (1343/6404, 1000G_30x)
delAG=0.2157 (1080/5008, 1000G)
delAG=0.2507 (1123/4480, Estonian)
delAG=0.2122 (818/3854, ALSPAC)
delAG=0.2303 (854/3708, TWINSUK)
delAG=0.1730 (317/1832, Korea1K)
delAG=0.232 (232/998, GoNL)
delAG=0.205 (123/600, NorthernSweden)
delAG=0.112 (24/214, Vietnamese)

Clinical Significance: Reported in ClinVar
Gene : Consequence: FAM20A : Non Coding Transcript Variant
PRKAR1A : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18520	AG=0.77441	=0.22559	0.598812	0.05	0.351188	0
European	Sub	14152	AG=0.76505	=0.23495	0.585924	0.055822	0.358253	0
African	Sub	2898	AG=0.8002	=0.1998	0.63078	0.030366	0.338854	3
African Others	Sub	114	AG=0.816	=0.184	0.666667	0.035088	0.298246	0
African American	Sub	2784	AG=0.7996	=0.2004	0.62931	0.030172	0.340517	3
Asian	Sub	112	AG=0.848	=0.152	0.714286	0.017857	0.267857	0
East Asian	Sub	86	AG=0.83	=0.17	0.674419	0.023256	0.302326	0
Other Asian	Sub	26	AG=0.92	=0.08	0.846154	0.0	0.153846	0
Latin American 1	Sub	146	AG=0.815	=0.185	0.643836	0.013699	0.342466	1
Latin American 2	Sub	610	AG=0.800	=0.200	0.645902	0.045902	0.308197	0
South Asian	Sub	98	AG=0.71	=0.29	0.469388	0.040816	0.489796	1
Other	Sub	504	AG=0.841	=0.159	0.706349	0.02381	0.269841	0

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	AG=0.791299	delAG=0.208701
gnomAD - Genomes	Global	Study-wide	139966	AG=0.784948	delAG=0.215052
gnomAD - Genomes	European	Sub	75822	AG=0.76860	delAG=0.23140
gnomAD - Genomes	African	Sub	41910	AG=0.79222	delAG=0.20778
gnomAD - Genomes	American	Sub	13638	AG=0.82981	delAG=0.17019
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	AG=0.8052	delAG=0.1948
gnomAD - Genomes	East Asian	Sub	3122	AG=0.8645	delAG=0.1355
gnomAD - Genomes	Other	Sub	2152	AG=0.7881	delAG=0.2119
14KJPN	JAPANESE	Study-wide	28258	AG=0.70118	delAG=0.29882
Allele Frequency Aggregator	Total	Global	18520	AG=0.77441	delAG=0.22559
Allele Frequency Aggregator	European	Sub	14152	AG=0.76505	delAG=0.23495
Allele Frequency Aggregator	African	Sub	2898	AG=0.8002	delAG=0.1998
Allele Frequency Aggregator	Latin American 2	Sub	610	AG=0.800	delAG=0.200
Allele Frequency Aggregator	Other	Sub	504	AG=0.841	delAG=0.159
Allele Frequency Aggregator	Latin American 1	Sub	146	AG=0.815	delAG=0.185
Allele Frequency Aggregator	Asian	Sub	112	AG=0.848	delAG=0.152
Allele Frequency Aggregator	South Asian	Sub	98	AG=0.71	delAG=0.29
8.3KJPN	JAPANESE	Study-wide	16760	AG=0.70567	delAG=0.29433
1000Genomes_30x	Global	Study-wide	6404	AG=0.7903	delAG=0.2097
1000Genomes_30x	African	Sub	1786	AG=0.7704	delAG=0.2296
1000Genomes_30x	Europe	Sub	1266	AG=0.7599	delAG=0.2401
1000Genomes_30x	South Asian	Sub	1202	AG=0.7704	delAG=0.2296
1000Genomes_30x	East Asian	Sub	1170	AG=0.8188	delAG=0.1812
1000Genomes_30x	American	Sub	980	AG=0.856	delAG=0.144
1000Genomes	Global	Study-wide	5008	AG=0.7843	delAG=0.2157
1000Genomes	African	Sub	1322	AG=0.7663	delAG=0.2337
1000Genomes	East Asian	Sub	1008	AG=0.8155	delAG=0.1845
1000Genomes	Europe	Sub	1006	AG=0.7535	delAG=0.2465
1000Genomes	South Asian	Sub	978	AG=0.766	delAG=0.234
1000Genomes	American	Sub	694	AG=0.844	delAG=0.156
Genetic variation in the Estonian population	Estonian	Study-wide	4480	AG=0.7493	delAG=0.2507
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	AG=0.7878	delAG=0.2122
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	AG=0.7697	delAG=0.2303
Korean Genome Project	KOREAN	Study-wide	1832	AG=0.8270	delAG=0.1730
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	AG=0.768	delAG=0.232
Northern Sweden	ACPOP	Study-wide	600	AG=0.795	delAG=0.205
A Vietnamese Genetic Variation Database	Global	Study-wide	214	AG=0.888	delAG=0.112

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 17	NC_000017.11:g.68540072_68540073del
GRCh37.p13 chr 17	NC_000017.10:g.66536213_66536214del
PRKAR1A RefSeqGene (LRG_514)	NG_007093.3:g.131450_131451del
FAM20A RefSeqGene	NG_029809.1:g.65882_65883del

Gene: FAM20A, FAM20A golgi associated secretory pathway pseudokinase (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAM20A transcript variant 3	NM_001243746.2:c.806-107_… NM_001243746.2:c.806-107_806-106del	N/A	Intron Variant
FAM20A transcript variant 1	NM_017565.4:c.1220-107_12… NM_017565.4:c.1220-107_1220-106del	N/A	Intron Variant
FAM20A transcript variant 2	NR_027751.2:n.	N/A	Intron Variant
FAM20A transcript variant X3	XM_006721959.4:c.806-107_… XM_006721959.4:c.806-107_806-106del	N/A	Intron Variant
FAM20A transcript variant X7	XM_011524918.4:c.	N/A	Genic Downstream Transcript Variant
FAM20A transcript variant X4	XM_017024781.3:c.	N/A	Genic Downstream Transcript Variant
FAM20A transcript variant X6	XM_047436319.1:c.	N/A	Genic Downstream Transcript Variant
FAM20A transcript variant X2	XR_934487.4:n.2482_2483del	N/A	Non Coding Transcript Variant
FAM20A transcript variant X1	XR_002958041.2:n.	N/A	Intron Variant
FAM20A transcript variant X5	XR_001752543.3:n.	N/A	Genic Downstream Transcript Variant
FAM20A transcript variant X8	XR_429905.3:n.	N/A	Genic Downstream Transcript Variant

Gene: PRKAR1A, protein kinase cAMP-dependent type I regulatory subunit alpha (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PRKAR1A transcript variant 5	NM_001276290.1:c.973+1007… NM_001276290.1:c.973+10071_973+10072del	N/A	Intron Variant
PRKAR1A transcript variant 4	NM_001276289.2:c.	N/A	Genic Downstream Transcript Variant
PRKAR1A transcript variant 6	NM_001278433.2:c.	N/A	Genic Downstream Transcript Variant
PRKAR1A transcript variant 7	NM_001369389.1:c.	N/A	Genic Downstream Transcript Variant
PRKAR1A transcript variant 8	NM_001369390.1:c.	N/A	Genic Downstream Transcript Variant
PRKAR1A transcript variant 1	NM_002734.5:c.	N/A	Genic Downstream Transcript Variant
PRKAR1A transcript variant 2	NM_212471.3:c.	N/A	Genic Downstream Transcript Variant
PRKAR1A transcript variant 3	NM_212472.2:c.	N/A	Genic Downstream Transcript Variant
PRKAR1A transcript variant X1	XM_011524984.4:c.	N/A	Genic Downstream Transcript Variant
PRKAR1A transcript variant X2	XM_047436369.1:c.	N/A	Genic Downstream Transcript Variant
PRKAR1A transcript variant X3	XM_047436370.1:c.	N/A	Genic Downstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: delAG (allele ID: 1226385 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001635753.5	not provided	Benign

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	AG=	delAG
GRCh38.p14 chr 17	NC_000017.11:g.68540072_68540073=	NC_000017.11:g.68540072_68540073del
GRCh37.p13 chr 17	NC_000017.10:g.66536213_66536214=	NC_000017.10:g.66536213_66536214del
PRKAR1A RefSeqGene (LRG_514)	NG_007093.3:g.131450_131451=	NG_007093.3:g.131450_131451del
FAM20A RefSeqGene	NG_029809.1:g.65882_65883=	NG_029809.1:g.65882_65883del
FAM20A transcript variant X2	XR_934487.4:n.2482_2483=	XR_934487.4:n.2482_2483del
FAM20A transcript variant X3	XR_934487.1:n.1909_1910=	XR_934487.1:n.1909_1910del
FAM20A transcript variant 3	NM_001243746.1:c.806-106=	NM_001243746.1:c.806-107_806-106del
FAM20A transcript variant 3	NM_001243746.2:c.806-106=	NM_001243746.2:c.806-107_806-106del
PRKAR1A transcript variant 5	NM_001276290.1:c.973+10071=	NM_001276290.1:c.973+10071_973+10072del
FAM20A transcript variant 1	NM_017565.3:c.1220-106=	NM_017565.3:c.1220-107_1220-106del
FAM20A transcript variant 1	NM_017565.4:c.1220-106=	NM_017565.4:c.1220-107_1220-106del
FAM20A transcript variant X3	XM_006721959.4:c.806-106=	XM_006721959.4:c.806-107_806-106del

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

51 SubSNP, 14 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss4475223	Jul 03, 2002 (106)
2	ABI	ss40770107	Mar 15, 2006 (126)
3	BCMHGSC_JDW	ss103600338	Dec 01, 2009 (131)
4	BUSHMAN	ss193458613	Jul 04, 2010 (132)
5	GMI	ss289335646	May 04, 2012 (138)
6	1000GENOMES	ss327802348	May 09, 2011 (138)
7	1000GENOMES	ss327929555	May 09, 2011 (138)
8	1000GENOMES	ss328228095	May 09, 2011 (138)
9	LUNTER	ss552538584	Apr 25, 2013 (138)
10	LUNTER	ss552894958	Apr 25, 2013 (138)
11	LUNTER	ss553624746	Apr 25, 2013 (138)
12	TISHKOFF	ss554877108	Apr 25, 2013 (138)
13	SSMP	ss664372170	Apr 01, 2015 (144)
14	EVA-GONL	ss993283236	Aug 21, 2014 (142)
15	1000GENOMES	ss1376871835	Aug 21, 2014 (142)
16	EVA_DECODE	ss1697332101	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1708828992	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1708829155	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1808858344	Sep 08, 2015 (146)
20	GENOMED	ss1968424107	Jul 19, 2016 (147)
21	JJLAB	ss2031346790	Sep 14, 2016 (149)
22	SYSTEMSBIOZJU	ss2629066692	Nov 08, 2017 (151)
23	GNOMAD	ss2951915401	Nov 08, 2017 (151)
24	SWEGEN	ss3015822851	Nov 08, 2017 (151)
25	MCHAISSO	ss3065660211	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3645462979	Oct 12, 2018 (152)
27	URBANLAB	ss3650690948	Oct 12, 2018 (152)
28	EGCUT_WGS	ss3682687455	Jul 13, 2019 (153)
29	EVA_DECODE	ss3700815588	Jul 13, 2019 (153)
30	ACPOP	ss3742172793	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3820138019	Jul 13, 2019 (153)
32	EVA	ss3834952408	Apr 27, 2020 (154)
33	KOGIC	ss3979196436	Apr 27, 2020 (154)
34	EVA	ss3986738741	Apr 27, 2021 (155)
35	TOPMED	ss5042171404	Apr 27, 2021 (155)
36	TOMMO_GENOMICS	ss5223249649	Apr 27, 2021 (155)
37	EVA	ss5237240399	Apr 27, 2021 (155)
38	1000G_HIGH_COVERAGE	ss5303758623	Oct 16, 2022 (156)
39	HUGCELL_USP	ss5496738997	Oct 16, 2022 (156)
40	1000G_HIGH_COVERAGE	ss5607779763	Oct 16, 2022 (156)
41	EVA	ss5624075215	Oct 16, 2022 (156)
42	SANFORD_IMAGENETICS	ss5660444890	Oct 16, 2022 (156)
43	TOMMO_GENOMICS	ss5779726384	Oct 16, 2022 (156)
44	EVA	ss5800210934	Oct 16, 2022 (156)
45	YY_MCH	ss5816685414	Oct 16, 2022 (156)
46	EVA	ss5834219090	Oct 16, 2022 (156)
47	EVA	ss5848456518	Oct 16, 2022 (156)
48	EVA	ss5851874539	Oct 16, 2022 (156)
49	EVA	ss5951841933	Oct 16, 2022 (156)
50	EVA	ss5980979539	Oct 16, 2022 (156)
51	EVA	ss5981303227	Oct 16, 2022 (156)
52	1000Genomes	NC_000017.10 - 66536213	Oct 12, 2018 (152)
53	1000Genomes_30x	NC_000017.11 - 68540072	Oct 16, 2022 (156)
54	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 66536213	Oct 12, 2018 (152)
55	Genetic variation in the Estonian population	NC_000017.10 - 66536213	Oct 12, 2018 (152)
56	gnomAD - Genomes	NC_000017.11 - 68540072	Apr 27, 2021 (155)
57	Genome of the Netherlands Release 5	NC_000017.10 - 66536213	Apr 27, 2020 (154)
58	Korean Genome Project	NC_000017.11 - 68540072	Apr 27, 2020 (154)
59	Northern Sweden	NC_000017.10 - 66536213	Jul 13, 2019 (153)
60	8.3KJPN	NC_000017.10 - 66536213	Apr 27, 2021 (155)
61	14KJPN	NC_000017.11 - 68540072	Oct 16, 2022 (156)
62	TopMed	NC_000017.11 - 68540072	Apr 27, 2021 (155)
63	UK 10K study - Twins	NC_000017.10 - 66536213	Oct 12, 2018 (152)
64	A Vietnamese Genetic Variation Database	NC_000017.10 - 66536213	Jul 13, 2019 (153)
65	ALFA	NC_000017.11 - 68540072	Apr 27, 2021 (155)
66	ClinVar	RCV001635753.5	Oct 16, 2022 (156)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs140180895	Apr 25, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss289335646, ss327802348, ss327929555, ss328228095, ss552538584, ss552894958, ss553624746, ss1697332101	NC_000017.9:64047807:AG:	NC_000017.11:68540071:AG:	(self)
72615419, 40236973, 28425703, 17927737, 15457658, 81218956, 40236973, 8894382, ss554877108, ss664372170, ss993283236, ss1376871835, ss1708828992, ss1708829155, ss1808858344, ss1968424107, ss2031346790, ss2629066692, ss2951915401, ss3015822851, ss3682687455, ss3742172793, ss3834952408, ss3986738741, ss5223249649, ss5624075215, ss5660444890, ss5800210934, ss5834219090, ss5848456518, ss5951841933, ss5980979539, ss5981303227	NC_000017.10:66536212:AG:	NC_000017.11:68540071:AG:	(self)
RCV001635753.5, 95305698, 512468371, 35574437, 113563488, 257717066, 5290548064, ss3065660211, ss3645462979, ss3650690948, ss3700815588, ss3820138019, ss3979196436, ss5042171404, ss5237240399, ss5303758623, ss5496738997, ss5607779763, ss5779726384, ss5816685414, ss5851874539	NC_000017.11:68540071:AG:	NC_000017.11:68540071:AG:	(self)
ss4475223, ss40770107, ss103600338	NT_010783.15:31810364:AG:	NC_000017.11:68540071:AG:	(self)
ss193458613	NT_010783.16:41604091:AG:	NC_000017.11:68540071:AG:	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs3214285

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs3214285